[Mristudio-users] Backprojecting template roi sets (TRS)

[Xin Li]

When you applied InvertedAIR to the roi file, the template will be the original image whose size is 128x128x66, not one of the JHU_MNI_SS atlas images any more.


Xin

----- Original Message -----
From: "Dorian P." <alb.net at gmail.com>
Date: Thursday, January 31, 2013 3:22 pm
Subject: Re: [Mristudio-users] Backprojecting template roi sets (TRS)
To: "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users at mristudio.org>
Cc: Xin Li <xli16 at jhmi.edu>, Yajing Zhang <zhangyajing9996 at gmail.com>, Jaymin Patel <jpatel18 at jhmi.edu>, Hangyi Jiang <hjiang at jhmi.edu>


> Yes, I have managed to see the rois by adjusting the view, but still can't
>  do the back projection. The manual matrix transformation
>  (Hmap->InvertedAIR) gives the result in  181x217x181 instead of my
>  128x128x66. See attached.
>  
>  Thank you.
>  
>  [image: Immagine in linea 1]
>  2013/1/31 susumu mori <susumu at mri.jhu.edu>
>  
>  > Hi Dorian,
>  >
>  > I think it is just a matter of display intensity. The ROI locations 
> have
>  > "1" and non-ROI pixels are "0". So, you have to right click on the 
> image
>  > (looks like blank) and adjust the display intensity scale to see 
> the dark
>  > ROIs (1 out of 256 grayscale is not visible).
>  >
>  > As for the batch processing of TRS to each subject data, we have
>  > executable codes.
>  > Xin and Hangyi, maybe we should post the executables somewhere in
>  > www.mristudio.org?
>  >
>  > Yajing, how did you apply the TRS to each subject? Did you use IDL 
> codes
>  > and the executables or did you use MriStudio one-by-one?
>  >
>  > On Thu, Jan 31, 2013 at 12:46 PM, Dorian P. <alb.net at gmail.com> wrote:
>  >
>  >> Hi,
>  >>
>  >> Just wanted to renovate this question. It is not clear to me how to
>  >> backproject TRS files, or whether I should do it for the whole 
> WMPM type II
>  >> atlas.
>  >>
>  >> The only way I could make atlas fiber tracking now is by projecting
>  >> tensors in normalized and by manually creating a .map file for 
> rois of a
>  >> fasciculus. The TRS that are for download don't work in DTIstudio.
>  >>
>  >> Thank you.
>  >>
>  >> Dorian
>  >>
>  >> 2013/1/30 Dorian P. <alb.net at gmail.com>
>  >>
>  >> Hi all,
>  >>>
>  >>> I am trying to do atlas based tract reconstruction based on Zhang 
> Yajing
>  >>> (2010) paper. I have performed LDDMM and need to backproject a 
> Template Roi
>  >>> Set (say the uncinate). The files in the TRS look like this:
>  >>>
>  >>> ROI_display.roihdr
>  >>> AND_#1.dat
>  >>> NOT.dat
>  >>> OR.dat
>  >>> ROI_display.dat
>  >>>
>  >>> I tried loading the these files in Diffeomap but there are no white
>  >>> pixels, all black. So, how ca I do this back projection?
>  >>>
>  >>>
>  >>> And is there an automatic way to massively invert TRS's in native 
> space
>  >>> or do I have to go one by one for each TRS to open and save in Diffeomap.
>  >>>
>  >>>
>  >>>  Thank you.
>  >>>
>  >>
>  >>
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